Defined characteristics of cathepsin B-like proteins from nematodes: inferred functional diversity and phylogenetic relationships

Molecular tools-advances, opportunities and prospects for the control of parasites of veterinary importance

The recent advancement in genome sequencing facilities, proteomics, transcriptomics, and metabolomics of eukaryotes have opened door for employment of molecular diagnostic techniques for early detection of parasites and determining target molecules for formulating control strategies. It further leads to the introduction of several purified vaccines in the field of veterinary parasitology. Earlier, the conventional diagnostic methods was entirely based upon morphological taxonomy for diagnosis of parasites but nowadays improved molecular techniques help in phylogenetic study and open an another area of molecular taxonomy of parasites with high precision. Control measures based upon targeting endosymbionts in parasites like Dirofilaria immitis is also under exploration in veterinary parasitology. Metagenomics have added an inside story of parasites bionomics which have created havoc in human and animals population since centuries. Omics era is playing a key role in opening the new approaches on parasite biology. Various newer generations of safer vaccines like edible vaccines and subunit vaccines and diagnostic techniques based upon purified immunologically active epitopes have become commercially available against the parasites (helminths, protozoa and arthropod borne diseases). Nowadays, a transgenic and gene knock out studies using RNA interference and CRISPR are also helping in understanding the functions of genes and screening of target genes, which are not available before the advent of molecular tools. Molecular techniques had paramount impact on increasing the sensitivity of diagnostic tools, epidemiological studies and more importantly in controlling these diseases. This review is about the advancements in veterinary parasitology and their impact on the control of these pathogens.

Differential proteolytic activity in Anisakis simplex s.s. and Anisakis pegreffii, two sibling species from the complex Anisakis simplex s.l., major etiological agents of anisakiasis

Proteolytic activity was studied in two sibling species of Anisakis (Nematoda: Anisakidae), A. simplex s.s. and A. pegreffii, throughout their in vitro development from third larval stage (L3) from the host fish (L3-0h) to fourth larval stage (L4) obtained in culture. Proteases have a significant role in the lifecycle of the parasite and in the pathogen-host relationship. Proteolytic activity peaks were detected at pH 6.0 and 8.5. Protease activity was detected in all the developmental stages of the two species studied at both pH values. These pH values were used for assaying with specific inhibitors which permitted the determination of metalloprotease activity, and, to a lesser extent, that of serine and cysteine protease. Aspartic protease activity was only detected at pH 6.0. At this pH, L4 larvae showed higher proteolytic activity than L3 larvae in both species (p < 0.001), the majority of activity being due to metalloproteases and aspartic proteases, which could be related to nutrition, especially the latter, as occurs in invertebrates. At pH 8.5, proteolytic activity was higher in A. simplex s.s. than in A. pegreffii (p < 0.01). At this pH, the majority of activity was due to metalloproteases in all developmental phases of both species, although, in L3-0h, the activity of these proteases was significantly higher (p < 0.03) in A. simplex s.s. than in A. pegreffii. This could be related to the greater invasive capacity of the former. Serine proteases have frequently been implicated in the invasive capacity and pathogenicity of some parasites. This may be related to the significantly higher activity (p ≤ 0.05) of serine protease in all the larval stages of A. simplex studied at pH 6.0. Thus, there are interspecific differences in proteases that have been related to pathogenesis in nematodes. These differences could thus be contributing to the previously reported differences in pathogenicity between these two Anisakis species.

Molecular expression and characterization of GCP7 gene of Haemonchus contortus

Haemonchus contortus is a highly pathogenic and most economically important parasite of sheep and goats worldwide. The cysteine proteases from H. contortus are prime targets for vaccine development. In the present communication we report the molecular expression and characterization of cathepsin B-like cysteine protease, GCP7 gene of H. contortus to study its efficiency as target protein for immunoprophylaxis against haemonchosis in sheep and goats. The complete ORF of GCP7 gene, devoid of the signal sequence, was amplified by RT-PCR from mRNA isolated from H. contortus and was cloned initially into pTZ57R/T cloning vector and then sub-cloned in the pET32a(+) expression vector to produce GCP7 antigen. The nucleotide and deduced amino acid sequence of the GCP7 was aligned against the related sequences of H. contortus available in public domain for in silico analysis by DNA STAR and MEGA version 4.0 softwares. The nucleotide sequence revealed that the GCP7 gene of H.contortus (Indian isolate) encodes 324 amino acids (devoid of signal sequence) and its nucleotide sequence had 95.9% to 99.4% sequence homology with that of U.S.A. and previously published Indian isolates. A high level expression of recombinant (r) GCP7 protein was observed in the molecular range (Mr) of 55 kDa. The rGCP7 protein was confirmed by its specific immunoreactivity against known reference positive sheep sera.

Proteases in blood-feeding nematodes and their potential as vaccine candidates

Parasitic nematodes express and secrete a variety of proteases which they use for many purposes including the penetration of host tissues, digestion of host protein for nutrients, evasion of host immune responses and for internal processes such as tissue catabolism and apoptosis. For these broad reasons they have been examined as possible parasite control targets. Blood-feeding nematodes such as the barber-pole worm Haemonchus contortus that infect sheep and goats and the hookworms, Ancylostoma spp. and Necator americanus, affecting man, use an array of endo- and exopeptidases to digest the blood meal. Haemoglobin digestion occurs by an ordered and partly conserved proteolytic cascade. These proteases are accessible to host immune responses which can block enzyme function and lead to parasite expulsion and/or death. Thus they are receiving attention as components of vaccines against several parasitic nematodes of social and economic importance.

Purification and characterization of cathepsin B-like cysteine protease from cotyledons of daikon radish, Raphanus sativus

Plant cathepsin B-like cysteine protease (CBCP) plays a role in disease resistance and in protein remobilization during germination. The ability of animal cathepsin B to function as a dipeptidyl carboxypeptidase has been attributed to the presence of a dihistidine (His110-His111) motif in the occluding loop, which represents a unique structure of cathepsin B. However, a dihistidine motif is not present in the predicted sequence of the occluding loop of plant CBCP, as determined from cDNA sequence analysis, and the loop is shorter. In an effort to investigate the enzymatic properties of plant CBCP, which possesses the unusual occluding loop, we have purified CBCP from the cotyledons of daikon radish (Raphanus sativus) by chromatography through Sephacryl S-200, DEAE-cellulose, hydroxyapatite and organomercurial-Sepharose. The molecular mass of the enzyme was estimated to be 28 kDa by SDS/PAGE under reducing conditions. The best synthetic substrate for CBCP was t-butyloxycarbonyl Leu-Arg-Arg-4-methylcoumaryl 7-amide, as is the case with human cathepsin B. However, the endopeptidase activity of CBCP towards glucagon and adrenocorticotropic hormone showed broad cleavage specificity. Human cathepsin B preferentially cleaves model peptides via its dipeptidyl carboxypeptidase activity, whereas daikon CBCP displays both endopeptidase and exopeptidase activities. In addition, CBCP was found to display carboxymonopeptidase activity against the substrate o-aminobenzoyl-Phe-Arg-Phe(4-NO(2)). Daikon CBCP is less sensitive (1/7000) to CA-074 than human cathepsin B. Expression analysis of CBCP at the protein and RNA levels indicated that daikon CBCP activity in cotyledons is regulated by post-transcriptional events during germination.

Advances in the sequencing of the genome of the adenophorean nematode Trichinella spiralis

The adenophorean nematodes are evolutionarily distant from other species in the phylum Nematoda. Interspecific comparisons of predicted proteins have supported such an ancient divergence. Accordingly, Trichinella spiralis represents a basal nematode representative for genome sequencing focused on gaining a deeper insight into the evolutionary biology of nematodes. In addition, molecular characteristics that are conserved across the phylum could be of great value for control strategies with broad application. In this review, we describe and summarize progress that has been made on the sequencing and analysis of the T. spiralis genome. The genome sequence was used in preliminary analyses for the investigation of specific questions relating to the biology of T. spiralis and, more generally, to parasitic nematodes. For instance, we evaluated an unusually large DNase II-like protein family, predicted proteins of prospective interest in the parasite-host muscle cell interaction, anthelmintic targets and prospective intestinal genes, the encoded proteins (potentially) linked to immunological control against other nematodes. The results are discussed in relation to characteristics that are broadly conserved among evolutionary distant nematodes. The results lead to expectations that this genome sequence will contribute to advances in research on T. spiralis and other parasitic nematodes.

Intestinal transcriptomes of nematodes: comparison of the parasites Ascaris suum and Haemonchus contortus with the free-living Caenorhabditis elegans

Background

The nematode intestine is a major organ responsible for nutrient digestion and absorption; it is also involved in many other processes, such as reproduction, innate immunity, stress responses, and aging. The importance of the intestine as a target for the control of parasitic nematodes has been demonstrated. However, the lack of detailed knowledge on the molecular and cellular functions of the intestine and the level of its conservation across nematodes has impeded breakthroughs in this application.

Methods and Findings

As part of an extensive effort to investigate various transcribed genomes from Ascaris suum and Haemonchus contortus, we generated a large collection of intestinal sequences from parasitic nematodes by identifying 3,121 A. suum and 1,755 H. contortus genes expressed in the adult intestine through the generation of expressed sequence tags. Cross-species comparisons to the intestine of the free-living C. elegans revealed substantial diversification in the adult intestinal transcriptomes among these species, suggesting lineage- or species-specific adaptations during nematode evolution. In contrast, significant conservation of the intestinal gene repertories was also evident, despite the evolutionary distance of ∼350 million years separating them. A group of 241 intestinal protein families (IntFam-241), each containing members from all three species, was identified based on sequence similarities. These conserved proteins accounted for ∼20% of the sampled intestinal transcriptomes from the three nematodes and are proposed to represent conserved core functions in the nematode intestine. Functional characterizations of the IntFam-241 suggested important roles in molecular functions such as protein kinases and proteases, and biological pathways of carbohydrate metabolism, energy metabolism, and translation. Conservation in the core protein families was further explored by extrapolating observable RNA interference phenotypes in C. elegans to their parasitic counterparts.

Conclusions

Our study has provided novel insights into the nematode intestine and lays foundations for further comparative studies on biology, parasitism, and evolution within the phylum Nematoda.

Biological properties of the nematode intestine warrant in-depth investigation, the results of which can be utilized in the control of parasitic nematodes that infect humans, livestock, and plants. Both the importance of intestinal antigens from Haemonchus contortus in immunity and the damage to H. contortus intestine by anthelmintic fenbendazole have highlighted the versatility of the intestine as an emerging target. However, biological information regarding fundamental intestinal cell functions and mechanisms is currently limited. Conserved intestinal genes across nematode pathogens could offer molecular targets for broad parasite control. Furthermore, qualitative and quantitative comparisons on intestinal gene expression among species and lineages can identify basic adaptations relative to a critical selective force, the nutrient acquisition. This study begins to identify intestinal cell characteristics that are conserved across representatives of two clades of nematodes (V and III) and further clarifies diversities that likely reflect species- or lineage-specific adaptations. Results consistent with functional data on digestive enzymes from H. contortus and RNAi in Caenorhabditis elegans, as examples, support the potential for the comparative genomics approach to produce practical applications. This study provides a platform on which extensive investigation of intestinal genes and a more comprehensive understanding of the Nematoda can be gained.

Gene discovery in the adenophorean nematode Trichinella spiralis: an analysis of transcription from three life cycle stages

Expressed sequence tags (ESTs) were produced from cDNA libraries for immature L1, mature muscle larva and adult stages of the adenophorean nematode Trichinella spiralis. 10,130 ESTs were grouped into 3454 gene clusters. The clusters represent a conservative estimate of 3262 unique genes. Interspecific comparisons of the predicted proteins support an ancient divergence of clade I nematodes from other nematodes in the phylum Nematoda. Furthermore, apparent clade I or Trichocephalida-specific proteins were identified, which may include molecular determinants important in the evolution of these species. Similarity matches identified 463 C. elegans genes homologs that confer phenotypes by RNA interference. Classification of predicted proteins suggested diverse cellular, metabolic and extracellular functions, significantly expanding the dataset of T. spiralis proteins with prospective, and potentially critical, functions. Several lines of evidence suggested stage-specific expression of certain genes beyond those previously identified. Evidence was obtained for the existence of large gene families encoding isoforms of known secreted proteins, such as p43 and TspE1. Unexpectedly, diverse isoforms of the muscle larva p43 gene appear to be expressed by immature L1. Proteinases, kinases, antioxidant proteins and enzymes involved in glycan synthesis are implicated in T. spiralis interactions with its hosts. Numerous genes were identified that encode predicted proteins in these categories. The genes discovered, when put into context of functional classification, stage of expression, and biology of the parasite, should substantially enhance experimental potential for research on this parasite.

mRNA sequences for Haemonchus contortus intestinal cathepsin B-like cysteine proteases display an extreme in abundance and diversity compared with other adult mammalian parasitic nematodes

Cathepsin B-like cysteine protease (cbl) genes produce the most abundant mRNAs ( approximately 16%) detected in the adult female intestine of the parasitic nematode Haemonchus contortus. CBL enzymes appear to digest host proteins and are vaccine candidates for immune control of H. contortus and potentially other parasitic nematodes. Hence, it is important to quantify the extent of diversity of H. contortuscbl genes. Here, expressed sequence tags (ESTs) were used to assess both the size and diversity of the H. contortuscbl gene family. Contig analysis of 686 cbl ESTs from a USA isolate resolved 123 clusters. ESTs were grouped into discrete sets and analyzed using an additive model. Discovery of new cbl clusters increased with each set and reached a terminal rate of about 1 per 10 ESTs. The extreme diversity was unique to cbls relative to other genes investigated and was ascribed to specific cbl clades. Sixty percent of cbl clusters from a UK isolate were shared with those identified in the USA isolate, suggesting conservation of cbl gene repertoires across regions, although minor to moderate geographic variation cannot be excluded. Sequence comparisons also suggested high potential for antigenic diversity among CBL proteins, which is relevant to vaccine strategies. Compared to other parasitic nematodes of mammals, the extreme abundance and diversity of intestinal cbl transcripts appear to be relative specializations for H. contortus. Therefore, adaptations related to nutrient acquisition may vary markedly among these parasitic nematodes.

Digestive proteases of blood-feeding nematodes

Blood-feeding parasites employ a battery of proteolytic enzymes to digest the contents of their bloodmeal. Host haemoglobin is a major substrate for these proteases and, therefore, a driving force in the evolution of parasite-derived proteolytic enzymes. This review will focus on the digestive proteases of the major blood-feeding nematodes - hookworms (Ancylostoma spp. and Necator americanus) and the ruminant parasite, Haemonchus contortus - but also compares and contrasts these proteases with recent findings from schistosomes and malaria parasites. Haematophagous nematodes express proteases of different mechanistic classes in their intestines, many of which have proven or putative roles in degradation of haemoglobin and other proteins involved in nutrition. Moreover, the fine specificity of the relationships between digestive proteases and their substrate proteins provides a new molecular paradigm for understanding host-parasite co-evolution. Numerous laboratories are actively investigating these molecules as antiparasite vaccine targets.

Family C1 cysteine proteases: biological diversity or redundancy?

Recent progress in the identification and partial characterization of novel genes encoding cysteine proteases of the papain family has considerably increased our knowledge of this family of enzymes. Kinetic data available to date for this large family indicate relatively broad, overlapping specificities for most enzymes, thus inspiring a growing conviction that they may exhibit functional redundancy. This is also supported in part by phenotypes of cathepsin knockout mice and suggests that several proteases can substitute for each other to degrade or process a given substrate. On the other hand, specific functions of one particular protease have also been documented. In addition, differences in cellular distribution and intracellular localization may contribute to defining specific functional roles for some of these proteases.

A novel cathepsin B active site motif is shared by helminth bloodfeeders

This study compared specific protein sequence motifs present within cathepsin B-like cysteine proteases from a number of helminth parasites. We have focused our efforts on cathepsin B-like proteases of Haemonchus contortus, Caenorhabditis elegans, Schistosoma mansoni, Schistosoma japonicum, Ostertagia ostertagi, and Ancylostoma caninum. The goal of this work is to correlate specific features, or proposed roles, of the cathepsin B-like proteases with primary sequence motifs discovered within the proteins. We report here a general motif for the identification of cathepsin B enzymes, and more significantly, a motif within this pattern that is found, with one exception, only in cathepsin B-like proteases of helminth bloodfeeders. We suggest that the "hemoglobinase" motif arose evolutionarily in a minimum of three independent events as a specialized response to increase the efficiency of hemoglobin degradation by these cathepsin B-like enzymes. This motif should be useful in identifying additional helminth hemoglobinases and may provide a specific target for drug design efforts.

Cathepsin B-like cysteine proteases and Caenorhabditis elegans homologues dominate gene products expressed in adult Haemonchus contortus intestine

Proteins expressed by nematode intestinal cells are potential targets for parasite control by immune or chemical based strategies. To expand our knowledge on nematode intestinal proteins, expressed sequence tags were generated for 131 cDNA clones from the intestine of adult female Haemonchus contortus. An estimated 55 distinct protein genes or gene families were identified. Predicted proteins represented diverse functions. Several predicted polypeptides were related to H. contortus proteins implicated in inducing protective immunity against challenge infections of this parasite. The dominant intestinal transcripts were represented by cathepsin B-like cysteine protease genes (cbl) (17% of protein coding expressed sequence tags (ESTs) analyzed). An estimated 11 previously undescribed cbl genes were identified, doubling the recognized members of this gene family. Multiple C-type lectin sequences were identified. Other notable sequences included a predicted Y-box binding protein, serine/threonine kinases and a cyclin E-like sequence. Predicted protein homologues were found in Caenorhabditis elegans for all but one H. contortus sequence (99%), while fewer homologues from other parasitic nematodes were found. Many of the proteases, lipase and C-type lectin homologues in C. elegans had apparent signal peptides, suggesting that they are secreted. Several gene products had no obvious similarity outside the phylum Nematoda. The ESTs identified intestinal genes with potential application to immune control, understanding of basic intestinal regulatory processes and refinement of nematode genomic resources.

The role of molecular biology in veterinary parasitology

The tools of molecular biology are increasingly relevant to veterinary parasitology. The sequencing of the complete genomes of Caenorhabditis elegans and other helminths and protozoa is allowing great advances in studying the biology, and improving diagnosis and control of parasites. Unique DNA sequences provide very high levels of specificity for the diagnosis and identification of parasite species and strains, and PCR allows extremely high levels of sensitivity. New techniques, such as the use of uniquely designed molecular beacons and DNA microarrays will eventually allow rapid screening for specific parasite genotypes and assist in diagnostic and epidemiological studies of veterinary parasites. The ability to use genome data to clone and sequence genes which when expressed will provide antigens for vaccine screening and receptors and enzymes for mechanism-based chemotherapy screening will increase our options for parasite control. In addition, DNA vaccines can have desirable characteristics, such as sustained stimulation of the host immune system compared with protein based vaccines. One of the greatest threats to parasite control has been the development of drug resistance in parasites. Our knowledge of the basis of drug resistance and our ability to monitor its development with highly sensitive and specific DNA-based assays for 'resistance'-alleles will help maintain the effectiveness of existing antiparasitic drugs and provide hope that we can maintain control of parasitic disease outbreaks.

Cathepsin B-like cysteine proteases confer intestinal cysteine protease activity in Haemonchus contortus

Cathepsin B-like cysteine protease genes (cbls) constitute large multigene families in parasitic and nonparasitic nematodes. Although expressed in the intestine of some nematodes, the biological and biochemical functions of the CBL proteins remain unresolved. Di- and tetra-oligopeptides were used as fluorogenic substrates and irreversible/competitive inhibitors to establish CBL functions in the intestine of the parasitic nematode Haemonchus contortus. Cysteine protease activity was detected against diverse substrates including the cathepsin B/L substrate FR, the caspase 1 substrate YVAD, the cathepsin B substrate RR, but not the CED-3 (caspase 3) substrate DEVD. The pH at which maximum activity was detected varied according to substrate and ranged from pH 5.0 to 7.0. Individual CBLs were affinity isolated using FA and YVAD substrates. pH influenced CBL affinity isolation in a substrate-specific manner that paralleled pH effects on individual substrates. N-terminal sequencing identified two isolated CBLs as H. contortus GCP-7 (33 kDa) and AC-4 (37 kDa). N termini of each began at a position consistent with proregion cleavage and protease activation. Isolation of the GCP-7 band by each peptide was preferentially inhibited when competed with a diazomethane-conjugated inhibitor, Z-FA-CHN(2), demonstrating one functional difference among CBLs and among inhibitors. Substrate-based histological analysis placed CBLs on the intestinal microvilli. Data indicate that CBLs are responsible for cysteine protease activity described from H. contortus intestine. Results also support a role of CBLs in nutrient digestion.